Hi Julie, apologies for the delayed response. Matt DeMaere here at UTS has looked into this issue and it appears to be a problem specific to recent versions of OpenJDK. Whereas the code will work command-line on the Sun Java VM without an X11 environment, the OpenJDK implementation of Java library functions used by the contig mover still require an X11 display. We are looking into how this can be fixed. In the meantime it's possible to work around the issue by using a Sun JDK or with the rather hackish approach of creating an X11 environment on the server with, e.g. VNC, that the contig mover can silently connect to.
Best, -Aaron On Wed, 2014-07-16 at 06:59 +1000, Julie Shay wrote: > Hi Aaron, > Thanks so much for your quick response. I know that Mauve is great for > genome alignments, and I find the contig mover very useful, which is > why I want to incorporate it into this pipeline. My coworkers and I > have tried to run the contig mover with both the most recent snapshot > and with snapshots shortly following the post I linked below, and we > keep getting similar errors. Here is an example of a command we've > been trying and the errors we've been getting: > > java -Djava.awt.headless=true -Xmx500m > -cp /home/jshay/Programs/mauve/mauve_snapshot_2011-12-16/Mauve.jar > org.gel.mauve.contigs.ContigOrderer -output 0093mauvetest -ref > 0093.gbk -draft 0093spades/contigs.fasta > Exception in thread "main" java.lang.NullPointerException > at > javax.swing.JFileChooser.isTraversable(JFileChooser.java:1596) > at > javax.swing.JFileChooser.setCurrentDirectory(JFileChooser.java:575) > at javax.swing.JFileChooser.<init>(JFileChooser.java:344) > at javax.swing.JFileChooser.<init>(JFileChooser.java:296) > at org.gel.mauve.gui.AlignFrame$1.<init>(Unknown Source) > at org.gel.mauve.gui.AlignFrame.<init>(Unknown Source) > at org.gel.mauve.gui.ProgressiveMauveAlignFrame.<init>(Unknown > Source) > at org.gel.mauve.contigs.ContigMauveAlignFrame.<init>(Unknown > Source) > at org.gel.mauve.contigs.ContigOrderer.init(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.<init>(Unknown Source) > at org.gel.mauve.contigs.ContigOrderer.main(Unknown Source) > > Do you know of something we might be doing wrong on our end? If we get > this to work, we can use a snapshot and reference the date stamp as > you suggest. Thanks again! > -Julie > > On 13/07/2014 7:43 PM, Aaron Darling wrote: > > > Hi Julie, > > There will be another release with a traditional numeric version > > identifier eventually, but as it currently stands the development > > snapshots are about as "stable" as research software gets. There are a > > number of cosmetic bugs but no major bugs that I am aware of in terms of > > the calculation of genome alignments. If you want to incorporate to your > > pipeline, I would suggest referencing the datestamp as the software > > version -- the snapshots will remain available to the public so that > > reproducibility of results by others can be achieved by obtaining a > > matching datestamped build of the software. > > > > Best, > > -Aaron > > > > On Fri, 2014-07-11 at 04:32 +1000, Julie Shay wrote: > > > Hi, > > > Are there currently any plans for an official release of a Mauve > > > update? We would like to use the Mauve Contig Mover from the command > > > line on our lab's cluster without an X-display, and I see that you've > > > done an unofficial update that allows this > > > ( http://sourceforge.net/p/mauve/mailman/message/28484265/ ), but I > > > was wondering whether your plans regarding a formal release have > > > changed in the past 2.5 years? We're trying to integrate the Mauve > > > Contig Mover into one of our pipelines, and we want to be confident > > > that the version we use is stable. Thanks! > > > -Julie > > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
